[module1]

;;path to speedseq package binary directory
$;SPEEDSEQ_BIN_DIR$; = /usr/local/packages/
;;Sequence file 1
$;Seq1File$; =
;;Sequence file 2
$;Seq2File$; =
;;Read Group
$;Read_Group$;='@RG\tID:NA12878\tSM:NA12878\tPL:ILLUMINA\tLB:NA12878\tPU:NA12878'
;;Reference
$;Reference$; =

[module2]

;;Output Chromosome
$;Chromosome$; = 
;;use --v for verbose summary
$;OTHER_ARGS$; = --v

##</code><code>##

[module1]

;;path to speedseq package binary directory
$;SPEEDSEQ_BIN_DIR$; = /usr/local/packages/
;;Sequence file 1
$;Seq1File$; = "USER_INPUT.txt"
;;Sequence file 2
$;Seq2File$; = "USER_INPT2.txt"
;;Read Group
$;Read_Group$;='@RG\tID:NA12878\tSM:NA12878\tPL:ILLUMINA\tLB:NA12878\tPU:NA12878'
;;Reference
$;Reference$; = "USER_INPUT_REF.txt"

[module2]

 ;;Output Chromosome
 $;Chromosome$; = "USER_INPUT_CHR.txt"
 ;;use --v for verbose summary
 $;OTHER_ARGS$; = --v

##</code><code>##

my ($template_name, $Prefix, $Seq1File,$Seq2File,$Align_Reference,$Chromosome_list,$Reference,$KnownSites ) = @ARGV;

GetOptions ('template_config=s' => \$template_name, 'Project=s' => \$Prefix, 'Fasta_seq1=s' => \$Seq1File, 'Fasta_seq2=s' => \$Seq2File, 'Ref_align=s' => \$Align_Reference, 'Chr_list=s' => \$Chromosome_list, 'Ref=s' => \$Reference, 'Sites=s' => \$KnownSites);


open my $in_fh, '<', $template_name;
my %field = map { s/^\s+|\s*\n$//g; $_; } grep { !/^\s*#|^\s*$/ }  <$in_fh>;
close $in_fh;


foreach my $spec (sort keys %field)
{
    if($spec =~ m/Output\s+Prefix/)
        {
        $field{$spec} = $field{$spec} .= $Prefix;
        }
        elsif ($spec =~ m/Sequence\s+file\s+1/)
        {
        $field{$spec} = $field{$spec} .= $Seq1File;
        }
        elsif ($spec =~ m/Sequence\s+file\s+2/)
        {
        $field{$spec} = $field{$spec} .= $Seq2File;
        }
        elsif ($spec =~ m/Align_Reference/)
        {
        $field{$spec} = $field{$spec} .= $Align_Reference;
        }
        elsif ($spec =~ m/Chromsome\s+List\s+file/)
        {
        $field{$spec} = $field{$spec} .= $Chromosome_list;
        }
        elsif ($spec =~ m/Reference/)
        {
        $field{$spec} = $field{$spec} .= $Reference;
        }
        elsif ($spec =~ m/Known\s+sites/)
        {
        $field{$spec} = $field{$spec} .= $KnownSites;
        }

}

# Print it to an output file

{
#open my $output_file = './test_processing.txt';
open my $out_fh, '>', './complete_nicu.txt';
foreach my $key (keys %field) {
    print $out_fh "$key\n";
    print $out_fh "$field{$key}\n";
   print "$field{$key}\n";
}
close $out_fh;
}